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Genome 189

Posted by timothy from the and-kede dept.
No One You Know writes "I just finished reading an excellent book by Matt Ridley called Genome. The book is divided into 23 chapters, one for each chromosome. The author picks a significant gene from each chromosome to focus on, and explores a myriad of topics such as why we age, how life forms assemble themselves into full-grown adults starting from a blob of cells, how we form and store new memories, and how gene therapy works. I found the book very well-written, highly interesting, and quite accessible. Anyone that is interested in knowing more about themselves and all life on Earth would do themselves a service to read it." Read on below for the remainder of NOYK's review.
Genome
author Matt Ridley
pages 352
publisher Harper-Collins
rating Excellent
reviewer No One You Know
ISBN 0060932902
summary The author selects one gene from each chromosome, and uses it to explain who we are and where we came from.

One thing Ridley discusses is how closely related humans are to many other species that seem quite unrelated. We share 99% of our genetic code with chimpanzees, which is more or less common knowledge. But we are also very similar to many other organisms, such as fruit flies. By comparing the genomes of different life forms, we can tell not only what creatures (and plants) we are related to, but historically when the genome split. Ridley explores possible explanations and ramifications of this knowledge (it's pretty hard to refute evolution with the facts he presents).

One of my favourite chapters in the book deals with self-assembly. How in God's green Earth do we develop into full-grown adults with a trillion cells, having started out as a tiny blob of a handful of cells? There are some really surprising discoveries here, such as the fact that the genes that lay out the general physical form of the body are laid out in order -- the gene for the head first, then the upper body, etc., ending with the rear. Another interesting fact is that the genes that define the front and back of a fruit fly also exist in humans, but are switched around. So the gene that defines the back of a fruit fly defines the front of a human, and vice versa. This means that at some point in our evolutionary history, one creature decided to walk on its front, and another decided to walk on its back.

Another chapter deals with why we age. Less than 50 cell divisions are required for us to grow into adults, but throughout life cell divisions are necessary for maintenance and repair. Each cell contains a complete copy of the genome; when a cell divides, it must make another copy for the new cell. However, the very beginning and end of each chromosome are not copied. In order to not lose important data, each chromosome has a long string of junk at the beginning and end. But with each cell division, a little more of the junk is lost and you get closer to cutting off the real data in the middle. In this way we've got a kind of built-in obsolescence; we are designed to live just long enough to bear and rear children.

One chapter is devoted to memory: how we create new memories and how we store them. Also discussed is the difference between instinct and learned knowledge, and why we need both. It turns out that language is a genetic thing; we have an instinctive capacity for language and we pick it up very easily as we develop. But then why is the vocabulary of a language not in our genes? Vocabulary is learned knowledge because if it weren't, it would be difficult for us to incorporate new words since they wouldn't be instinctive. Basically, as I understand it, static knowledge is often recorded in our genes (therefore becoming instinct), while dynamic knowledge must be learned.

Ridley dedicates one chapter to gene therapy and modification: how it works and the ethical concerns. I was curious as to how injecting a new or repaired gene into the cell of an organism could affect anything but that one cell. It turns out there are enzymes that will replicate the new DNA strand and go around distributing it to other cells -- a virus! Geneticists use the code from a virus that causes replication (leaving the bad stuff of course) and combine it with the DNA they want to repair or replace in an animal. They then "infect" the animal with the new code.

In short, I found Matt Ridley's "Genome" a fascinating book. The mapping of the human genome was a huge milestone in human history, and Ridley does an excellent job of using it to explain in layman's terms who and what we are. What we don't know about the genome dwarfs what we do know of course, and Ridley makes no bones about that point. But the bit that we do know just makes you sit back in awe. Ridley has a talent for translating his own enthusiasm for the subject to the written word.

You can purchase Genome from bn.com. Slashdot welcomes readers' book reviews -- to see your own review here, read the book review guidelines, then visit the submission page.
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Genome

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  • No wonder... (Score:3, Funny)

    by yeoua ( 86835 ) on Monday August 12, 2002 @10:26AM (#4054291)
    "Another interesting fact is that the genes that define the front and back of a fruit fly also exist in humans, but are switched around. So the gene that defines the back of a fruit fly defines the front of a human, and vice versa. This means that at some point in our evolutionary history, one creature decided to walk on its front, and another decided to walk on its back."

    So would that mean that the fly's equivalent of a head is a human's equivalent of a butt? No wonder flies are so ugly.

    On the same note... one wonders if this same backwards thing applies to the pointy hair boss species of the human race.
    • Not exactly, Walking is more of a behavioral thing.
      And the reason why small changes in the gentic code produce such drastic changes is that the information coefficent of genetic code is high.
      What may seem to a layperson as one little change here and there is actually very very big in terms of nature.
      "On the same note... one wonders if this same backwards thing applies to the pointy hair boss species of the human race.
      Not exactly! But its funny ;-)
    • So would that mean that the fly's equivalent of a head is a human's equivalent of a butt?

      No, it's a different axis -- the back of the fly's head is the equivalent of the front of the human's head. (Dorsal/ventral axis, not anterior/posterior.)

      Speaking _extremely_ loosely, of course. ;-)

    • oh, is the "back" gene this one [nih.gov] or this one [nih.gov] by any chance?
  • 50 cell divisions - assuming that each cell lives for the duration of all divisions would yield 1,125,899,906,842,624 cells. Don't know if I would have put it in the terms of "only" 50 divisions. My only experience with this book being the review, I'm not sure that this applies, but I'm always a bit disappointed with books like this. Explaining the genome is all well and good, but I always want to see more "what-if" scenarios. Like would it be possible to make a fruit fly 50% bigger or something.
    • Well, that's misleading math. First off, not every cell divides every time. Some organs, like eyes, stop or slow cell division once they reach a certain point. Others keep dividing rapidly throughout the life of the organism.

      Another thing is controlled apoptosis, which is cell suicide. This is very very common in development, and is necessary to get the organism to look the way it does. That's why you've got fingers instead of webs. You know the little webs at the base of the area between your digits? Those are remnants of the cells that died during your development. Many of the cells that did divide continually go through apoptosis, so they're not around in the mature organsim.

      And I don't know about making flies 50% bigger, although I'd be willing to bet a lot on it's having been done (I hate working with the little buggers myself, so I don't really keep up on them) but I know for a fact that it's been done in mice and plants. Maybe not 50% bigger, but definitely bigger.
  • 1. I like to program
    2. I like to spend lots of time with linux
    3. I like to spend lots of time on Slashdot
    4. I chase karma
    5. I am witty
    6. I like to drink
    7. I like to smoke
    8. I like to program
    9. See 1.
    10. I don't understand girls
    11. I don't like the sun
    12. I like the Matrix
    13. I thrive on violent games and movies
    14. I don't like fighting for real
    15. I shower when I have to
    16. I optimise my housework
    17. I like girls, but they don't understand me
    18. I do bad things to myself but not to others
    19. No-one gets that
    20. I want to meet aliens
    21. I want them to be nice
    22. I want to be alive when BattleMechs are invented.
    23.???

    Oh, crap, I'm a code from Mars and you have to guess the 23rd chromosome.
  • If you never thought you'd read a book about genetics, (or even if you have) then this is the book for you. Ridley shows how the genetic map that is being developed for us will lead us to many of the answers that we have sought about ourselves. He explains in basic terms how genetics and evolution works. The most amazing part of this book is that it is extremely enjoyable to read. While still in the second chapter I was contemplating reading it again. If you have any interest in how we got to be what we are and what the future may hold for us, (or if you want some great party trivia) then reading 'Genome' will be both entertaining and enriching.

    -dk
  • Let me start this by saying that I enjoyed the book. But should books be held to a different standard than movies regarding reviews? I remember a recent review of U571 getting a bunch of shit because it was years late. Since the time that this book was written the entire genome has been mapped. In such a volatile field there are many things that go out of date fast. Maybe it's one thing to see a review of The Selfish Gene which although is 25 years old established an entirely new field of study, but this isn't groundbreaking material despite being well written and I'm pretty certain some of this material is out of date. I hope to not see a review of Misery or Hyperion any time soon on /.
  • Beauty is the first test; there is no permanent place in the world for ugly mathematics.
    G.H. Hardy

    This reminds me that God is a wonderfull mathematician. :)

  • Ridley (Score:2, Interesting)

    by HoldenCaulfield ( 25660 )
    Some of you might be interested to see that Ridley is also into crop circles [sciam.com] . . .

    I was rather surprised to come across that article in Scientific American . . . I had two classes that we used Genome in. The first was called Science and Society and we basically sat around for three hours a week discussing the issues, parties, consequences, and obligations of such topics as AI, intellectual property (Napster was in it's prime at this point), genetically engineered crops, etc etc. Was a cool class, as we had some good discussions, did some role playing (i.e. one group of students is a local town board, another is a group from Monsanto trying to bring in genetically engineered crops, and the rest of the class was town people). Was also interesting as we had a good mix of religous/scientific/somewhere in the middle people, so we had lots of good view points presented.

    The second class, taught by the same professor, was on human diversity, and we used select chapters from the book to examine nature verses nurture, and to try and determine some of the reasons for the differences amongst people and how one might define what a human being is . . .

    ernie
    • Some of you might be interested to see that Ridley is also into crop circles [sciam.com] . . .

      Uhhhhh jah! That's a nice balanced way of putting it ... he's "into" crop circles. Did you even read that article? He's "into" showing that crop circles are a load of bullplop -- not exactly the same thing now is it?

  • Interesting but with substantial flaws (Score:3, Informative)

    by Cirkit ( 584149 ) on Monday August 12, 2002 @10:42AM (#4054380)
    Although Genome is an interesting read, there are some significant flaws that caused me to question whether the author knew what he was talking about.

    One of the highlights:

    (page 267 in my text - or look up Affymetrix in your index.) The author says "The technology is already being developed, by a small Californian company called Affymetrix among others, to put a whole gemnome-full of genetidc sequences on a single silicon chip. One day we might each carry with us exactly such a chip from which the doctor's computer can read any gene the better to tailor his prescription to us." This is so mangled as to be almost hilarious. Affy IS putting DNA sequences on chips (as are several other companies) with the idea that you could look for disease markers by looking at whether or not an individual's DNA (or RNA) can pair with it (base pairing, right?). There's some interesting potential here for diagnostics and appropriate drug targeting.

    Ok up to here. But THEN the author takes the idea of having your medical records on a card and totally mashes it in. Trust me, you will NOT carry in the "chip" (which is NOT a chip like you might imbed in a smart card) to your Dr's office. Stupid stupid stupid. To the best of my knowledge (I don't work there), Affy isn't working on medical record storage, which is what the author is suggesting.

    The best part here is that the references are articles in the Financial Times and New Scientist (which is NOT a scientific journal, don't get confused by the name). So Ridley read the popular press without any real understanding, and then mangled things up some more on his own.

    I appreciate that the author is trying to write a book on a tough subject for a general audience, but I question whether the author actually understands this tough subject himself.

    I had several other spots in Genome where there were obvious flaws, but I can't put my finger on them at the moment. The feeling I got from this text when it strayed into areas I knew less well was "Wow! I didn't know that. Of course, I still don't believe that."

    • I agree that it is a decent book, but its important to take into account that Ridley is a journalist, not a biologist. One of the main problems with books like this is that they tend to over-emphasize sequencing, supposing that having the sequence, or even understanding it, is sufficient to understand the organism.

      To get a more balanced view from a brilliant source, read R. C. Lewontin "The Triple Helix" and/or "Biology as Ideology".
    • What you describe would be wrong, but also not what the author is trying to say. :)

      The idea here has nothing to do with medical records, the point is that these chips (not necessarily carried on you, nor "read by a computer", at least not directly) allow to quickly test for specific genetic markers, or for specific genes being up-/downregulated. Which, can tell a whole lot about how effective specific drugs will be on this individual. This is an emerging area in diagnostics.

    • some significant flaws that caused me to question whether the author knew what he was talking about

      The above comment is completely ridiculous, and a perfect example of troll (-1). All Ridley was trying to say is that diagnosis of a complete human genome using only a single chip will have profound medical implications. In this he is completely right. Ofcourse, he uses popular views and simple explanations of complex things, so that your uncle Billy Bob will be able to grasp them.

      Having a Ph.D. and lots of years research experience in human genetics, I can say the book contains a couple of these slightly incorrect details. That doesn't stop normal people from getting the general idea. It certainly did not stop me from giving a copy to my uncle Billy Bob. Journalism has never been an exact science. I think it is a wonderful book, very rich in detail. Everyone should read it.

  • Hollywood needs this book air-dropped (Score:3, Insightful)

    by totallygeek ( 263191 ) <sellis@totallygeek.com> on Monday August 12, 2002 @10:59AM (#4054463) Homepage
    Hollywood movies have been getting cloning and gene technology wrong for decades. Most people there believe cloning to be what they saw performed by Marvin Martian where a pill goes into a machine and stamps out an adult life-form. I know it is entertainment, but they don't screw up THAT bad with everything else!

    • Well, I'd say they botch up computers and the internet, particularly security, pretty bad.

      Besides, I think that ever since Dolly, a good number of people understand, at least vaguely, some of the basic principles of how cloning is done (take DNA from a cell of the parent, put it in to an egg, and put it in a surrogate mother). Granted, few understand the complexities involved in this, like the absolute need to reprogram the genome, and the incredibly high failure rate that goes along with it, not to mention the fact that these organisms aren't clones at all, but chimeras (mitochondrial DNA).

      But then, I wouldn't expect or want Hollywood to educate the general public on those things. Besides, I don't think Hollywood wants the job, nor do I think that the public wants it of Hollywood. That's the job of scientists and journalists working together.

  • Is that all cloning needs to overcome? (Score:4, Interesting)

    by mblase ( 200735 ) on Monday August 12, 2002 @11:04AM (#4054492)
    Each cell contains a complete copy of the genome; when a cell divides, it must make another copy for the new cell. However, the very beginning and end of each chromosome are not copied. In order to not lose important data, each chromosome has a long string of junk at the beginning and end.

    IIRC, the problem with the Dolly sheep clone, genetically speaking, is that the clone aged too quickly; genetically, she was as old as her "mother", even though physiologically she was newly born.

    Is this the only problem we need to overcome, then? Figure out how much "junk" DNA needs to be added to each end of the chromosome, make it up in a molecular blender, and go to it? Why, we could make humans live twenty or fifty years longer by padding their DNA before birth using the same strategy.
    • "Each cell contains a complete copy of the genome; when a cell divides, it must make another copy for the new cell. However, the very beginning and end of each chromosome are not copied. In order to not lose important data, each chromosome has a long string of junk at the beginning and end."

      IIRC, the problem with the Dolly sheep clone, genetically speaking, is that the clone aged too quickly; genetically, she was as old as her "mother", even though physiologically she was newly born.

      Is this the only problem we need to overcome, then? Figure out how much "junk" DNA needs to be added to each end of the chromosome, make it up in a molecular blender, and go to it? Why, we could make humans live twenty or fifty years longer by padding their DNA before birth using the same strategy.

      The body already has a way to re-add the junk, for use in the germ cells (precisely to stop the dolly problem).

      I think the purpose of the limit on replications is to stop cancers, etc. Bit hazy on this, but IIRC this is one of the safety measures that protects us from over ambitious cells...

    • Telomeres (Score:3, Insightful)

      by krmt ( 91422 )
      Why, we could make humans live twenty or fifty years longer by padding their DNA before birth using the same strategy.
      Funny, that sounds like cancer.

      Cancerous cells don't have problems with their telomeres, which is why they can be immortal (they have a lot of other things wrong with them too, but this is important). Adding to the lengths of telomeres artificially would have to be very very very well controlled in order to avoid the risk of cancer.

      I personally don't think telomeres are all that there is that's related to aging anyhow. Cell death simply doesn't explain everything that happens to a person in their old age, the same way simple cell division doesn't explain how you can get a full organism from a single cell. Aging is a process, and allowing your cells to replicate a another 10 or 20 cycles isn't going to stop that process entirely. This is all my own personal (and somewhat informed) opinion, but I think if people do start to add extra length to their telomeres, they're going to find that it's not the fountain of youth at all.
  • In the past few months I've embarked on a journey to get into the biotech industry (specifically bioinformatics). I picked this book up at Half Priced Books in Austin, TX and I thought it was an amazing primer to a field that I haven't read about since 9th grade biology. I'm completely hooked now. Ridley really does an excellent job explaining the subject in a pallatable language.

  • Great book (Score:1, Informative)

    by Anonymous Coward
    Genome is indeed a wonderful read. I recommend it to anyone who is looking for a quick and dirty guide to the oftentimes complex world of genetics. Although there are some parts that make me question the author's knowledge of the subject (such as the chapter on the gene that controls the size of the male genitalia--Ridley claims that the penis is generally smaller and more prone to impotence in those whose intellect leans more towards technology and science.. but I digress), overall, it is a great book.

    Easy to pick up and read (I was so caught up in the book, I ended up finishing it completely on a recent 2-hour business flight to Paris) and full of great wit and excellent observations, I don't think any regular /. visitor would go wrong in going out and picking this little gem up.
  • Humans have 46 chromosomes. 44 of them are paired for all humans, but one of them (X) is only paired for women, while men have another (Y) instead of the second X.

    So women have 23 different chromosomes (all paired), while men have 24 (22 paired, one X, one Y).

    So if the book only covers 23 chromosomes, it covers exactly the number of different chromosomes women have, but leaves out one chromosome men have. Therefore I conclude it must be a feministic book. :-)
  • I recommend reading his book on game theory and virtue: "The Origins of Virtue" and his book on sex w/r/t evolution: "The Red Queen". They are each very readable and thorougly fascinating. I wish he would write more...

    -c
  • genome and kede

    hahahah, that is funny. Someone mod Timothy up as +1 Funny, please.
  • I read "Genome" because I'm a fan of his previous two books, "The Red Queen" [amazon.com] (on the evolution of sex) and "The Origins of Virtue" [amazon.com] (how did cooperation evolve?). Both are well written and accessible to the layperson and get my recommendation, although they could use an update - they date from the early and middle 90s respectively - and "The Origins of Virtue" suffers from Mr. Ridley's thatcherist views on politics.

    As for "Genome" - I liked it, but since I had read a few pop sci books about genetics before it, I didn't learn many new things. Still, I don't regret buying it.

    If I had to choose between the tree books, I would pick "The Red Queen". I bought Dawkins' "The Selfish Gene" and Ridley's "The Red Queen" on the same day, and I couldn't put down either of them. Recommended, but YMMV.
  • Genome is not a very new book (genetics is changing faster than cs, believe it or not) and so I wouldn't read it for the nitpicky details. Its meant to give a bird's eye view of what's going in this field for the neophytes among us (and perhaps for some geneticists as well).
    I thought the premise of the book was great but it dragged on a little bit (quite a bit actually) in the last few chapters where his arguments are not very clear.
    Overall, if you don't know anything about genes (realisticaly speaking) this is a good book, at least read the first three quarters.
  • I've often heard the claim that humans share x% of their DNA with another species... but what does this actually mean? First, how do you define the "typical" human (or chimp, or banana) genome? And second, given two "typical" genomes, how do you determine the degree of similarity between two strings of different lengths?

    Another claim I've often heard is that the genetic differences between individuals of the same race are greater than the genetic differences between races. Does this claim have any statistical meaning? How do you find a typical genome for a race, especially since racial categories are so fuzzy?

    I'd be grateful if someone whose knowledge of genomics extends beyond reading The Selfish Gene could shed some light on these questions. :)

    • Another claim I've often heard is that the genetic differences between individuals of the same race are greater than the genetic differences between races. Does this claim have any statistical meaning? How do you find a typical genome for a race, especially since racial categories are so fuzzy?

      L. L. Cavalli-Sforza's Genes, People and Languages [amazon.com] is a good, short and accessible introduction into the modern line of thinking in population genetics. If you're really into it, there's also The History and Geography of Human Genes [amazon.com] by the same author, but at 1088 pages full of formulas and diagrams, this is not exactly what I'd call light reading. 8-)

    • I've often heard the claim that humans share x% of their DNA with another species... but what does this actually mean? First, how do you define the "typical" human (or chimp, or banana) genome?

      The 98/99% similarity figure is pretty widely quoted, but is at best a handwaving estimate meaning little more than "really really similar". It actually does come out of early genome analysis work, but the figure is pretty rough.

      I don't know what your level of familiarity with genetics is, but you're likely aware that DNA is a double-strand and both strands can be unwound and used as a template to generate a copy of their opposite number.

      Similarly, two single-stranded DNA molecules which are placed in solution with one another under the right conditions will "anneal" together to form a double-helix again, provided that their base sequences are complementary.

      The ease with which they do this is a measure of how similar their sequences are.

      And that is the basis of the 98% figure. Put human and chimp DNA together, melt the strands apart (just by heating) and then measure the rate at which they anneal to one another to get a measure of their similarity. Clearly I'm simplifying the process here, but that's the general idea.

      Of course this early primitive work has been strongly supported by the large number of actual gene sequences available now for chimp and human, by which we can get a direct view of how similar they are.

  • I am missing a few (Score:3, Funny)

    by Tablizer ( 95088 ) on Monday August 12, 2002 @12:22PM (#4055222) Journal
    Has he identified the "people-skills" gene? I seem to be missing it (or have it toggled off). I find very little interest in talking about food, movies, gossip, clothes, golf, and lots of others.

    Also, I am missing the OOP gene. I don't get why people think OOP is so great. It is inferior to good procedural/relational modeling and "noun managment" IMO. GOF is hard-wired indexes to me, primative. (Either that, OOP fans lack a procedural/relational gene.)(oop.ismad.com)
  • ...the gene the makes everyone think that we are made up of genes? just wonderin'...

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